Merge branch 'main' into marlene

Glycine/max/wip_marlene/Cai_Wang_2017.yml

@@ -213,3 +213,4 @@ references:
   - citation: Yang, Lan et al., 2022
     doi: 10.1111/jipb.13207
     pmid: 34962095
+

Glycine/max/wip_wei/Head_Galos_2012_traits.yml

@@ -1,20 +1,20 @@
 ---
 gene_symbols:
   - KASII-A
-gene_symbol_long: beta-ketoacyl-ACP synthase II 
-gene_model_pub_name: Glyma17g05200 
+gene_symbol_long: beta-ketoacyl-ACP synthase II
+gene_model_pub_name: Glyma17g05200
 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma17g05200
 confidence: 3
 comments:
   - Mutations in the soybean 3-ketoacyl-ACP synthase gene are correlated with high levels of seed palmitic acid
-phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control 
-traits: 
+phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control
+traits:
   - entity_name: beta-ketoacyl-acyl-carrier-protein synthase II activity
     entity: GO:0033817
 references:
   - citation: Head, Katie, et al., 2012
-    doi: 10.1007/s11032-012-9707-x 
-    pmid: null 
+    doi: 10.1007/s11032-012-9707-x
+    pmid: null
 
 ---
 gene_symbols:
@@ -23,8 +23,8 @@ gene_symbol_long: plastid 3-keto-acyl-ACP synthase II-B
 gene_model_pub_name: Glyma13g17290
 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g17290
 confidence: 3
-phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control 
-traits: 
+phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control
+traits:
   - entity_name: beta-ketoacyl-acyl-carrier-protein synthase II activity
     entity: GO:0033817
 references:

Phaseolus/vulgaris/wip_marlene/phavu_Davila-Delgado_Flores-Canul_2023.yml

@@ -0,0 +1,29 @@
+---
+gene_symbols:
+  - SYMRK (in Phaseolus vulgaris, Lotus japonicus, and Arachis hypogaea)
+  - DMI2 (in Medicago truncatula)
+  - NORK (in Medicago sativa)
+gene_symbol_long: SYMbiosis Receptor-like Kinase
+gene_model_pub_name: Phvul.002G143400
+gene_model_full_id: phavu.G19833.gnm1.ann1.Phvul.002G143400
+confidence: 5
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - SYMRK is activated in root hairs by phosphorylation in response to the perception of NOD factors
+  - SYMRK-EGFP (enhanced green fluorescence protein) is endocytosed from the plasma membrane to intracellular puncta and affects the SYMRK signaling pathway
+  - SYMRK-suppressed mutants can't form infection threads and therefore can't form functional nodules, though they do form pseudo-nodules lacking symbiotic bacteria and fungi
+  - SYMRK overexpressing mutants form non-functional nodules without rhizobia
+phenotype_synopsis: SYMRK is necessary for nodule organogenesis.
+traits:
+  - entity_name: bioloical process involved in symbiotic interaction
+    entity: GO:0044403
+  - entity_name: kinase activity
+    entity: GO:0016301
+  - entity_name: positive regulation of receptor-mediated endocytosis
+    entity: GO:0048260
+references:
+  - citation: Dávila-Delgado, Flores-Canúl, et al., 2023
+    doi: 10.1007/s00425-023-04116-0
+    pmid: 36928335
+

Vigna/radiata/wip_marlene/vigra_Liu_Zhang_2022.yml

@@ -0,0 +1,24 @@
+---
+gene_symbols:
+  - CCA1L26
+gene_symbol_long: Circadian Clock Assoicated 1 Like 26
+gene_model_pub_name: Vradi05g00310
+gene_model_full_id: vigra.VC1973A.gnm6.ann1.Vradi05g00310
+confidence: 3
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - VrCCA1L26 shares homology with AtCCA1, AtLHY, and GmLCL genes.
+  - In transgenic Arabidopsis, VrCCA1L26 delays flowering time by supressing Constans (CO), Flowering locus T (FT), Supressor of Overexpression of Constans 1 (SOC1), and Timing of Cab Expression 1 (TOC1).
+  - VrCCA1L26 expression is affected by photoperiod and is supressed by expression of TOC1.
+  - VrCCA1L26 may play a role in isoflavonoid synthesis, stress response, hypocotyl growth, seed germination, and leaf senescence. This has not been experimentally validated.
+phenotype_synopsis: VrCCA1L26 delays flowering time in transgenic Arabidopsis thaliana, but its function in Vigna radiata has not been experimentally validated.
+traits:
+  - entity_name: transcription factor binding
+    entity: GO:0008134
+  - entity_name: photoperiod-sensitive flowering time trait
+    entity: TO:0000934
+references:
+  - citation: Liu, Zhang, et. al., 2022
+    doi: 10.1186/s12864-022-08620-7
+    pmid: 35581536

templates/Example.yml

@@ -1,6 +1,6 @@
 ---
 # DIRECTIONS
-# As your first curation assignment, read the paper Tang, Su et. al., 2017 (doi: 10.1093/jxb/erw425).
+# As your first curation assignment, read the paper Tang, Su et al., 2017 (doi: 10.1093/jxb/erw425).
 # Create your own yml file based on the blank and annotated templates below.
 # Name your new file "Tang_Su_2012_practice.yml."
 # When you are done, compare your yml file to the Answer Key provided below.
@@ -36,10 +36,10 @@ gene_symbols:
   -  # If there are multiple names for one gene, enter them on separate lines with the most common name listed first.
   -  # If more than one gene is described in the same paper, paste another copy of this template at the bottom of your document and fill it in for the second gene.
 gene_symbol_long:  # The long-hand version of the gene_symbol acronym, e.g. "Nodule Number Control 1" (do not include the prefix Glycine max).
-gene_model_pub_name:  # REQUIRED; This should be listed in the publication in the format "GlymaXXgXXXXX," e.g. "Glyma12g07800".
-# If the paper has no "GlymaXXgXXXXX," try one of the search methods described at the bottom of this document.
+gene_model_pub_name:  # REQUIRED; This should be listed in the publication, e.g., Glyma02g17170.2, SoyW82_02G152800.1, or Glyma.02G152800, depending on the annotation version.
+# If the paper has no gene model name (rather, has a gene symbol plus sequence) try one of the search methods described at the bottom of this document.
 gene_model_full_id:  # REQUIRED; The gene name in Legume Information System. It looks like "glyma.Wm82.gnm2.ann1.Glyma.12G078000".
-# Find it by entering your gene_model_pub_name into the "Identifier" search box on this website: https://jekyll.dev.lis.ncgr.org/tools/search/gene.html
+# Find it by entering your gene_model_pub_name into the "Identifier" search box on this website: https://www.legumeinfo.org/tools/search/gene.html
 confidence:  # A value from 1 to 5 showing how strong the evidence for the gene's function is.
 # See the bottom of the document for guidance on assigning a confidence level.
 curators:
@@ -51,7 +51,7 @@ comments:
 phenotype_synopsis:  # Briefly describe the phenotype, e.g. "NNC1 is a transcription factor that negatively regulates nodule number by repressing GmENOD40."
 traits:  # REQUIRED; at least one "entity" ontology accession describing the function of the gene. Find ontologies by searching this database: https://www.ebi.ac.uk/ols/ontologies
   - entity_name:  # The name of the ontology accession, e.g. "nodulation"
-    entity:  # The ontology accession code, e.g. "GO:0009877." Those that begin with "GO" are plant traits.
+    entity:  # The ontology accession code, e.g. "TO:0000898", with "TO" indicating the Trait Ontology
   - quality_name:  # Optional; quality ontologies can be used to describe properties of the trait, e.g. "premature."
     quality:  # Quality ontology codes usually begin with "PATO"
   - relation_name:  # Optional; Relations ontologies can be used to describe the effects of the trait, e.g. "negatively regulates."
@@ -60,8 +60,7 @@ traits:  # REQUIRED; at least one "entity" ontology accession describing the fun
     entity:  # Code of additional ontology.
     # You can add more lines describing the qualities and relations of your additional ontology entities.
 references:  # REQUIRED; At least one citation with its doi or pmid. Ideally, include several citations.
-  - citation:  # The primary paper you extracted information from. Use the "LastName, LastName et al., YEAR" format, e.g. "Wang, Wang et. al., 2014"
-    doi:  # the bare doi (omit https://doi.org/), e.g. "10.1105/tpc.114.131607," not "https://doi.org/10.1105/tpc.114.131607"
+  - citation:  # The primary paper you extracted information from. Use the "LastName, LastName et al., YEAR" format, e.g. "Wang, Wang et al., 2014"    doi:  # the bare doi (omit https://doi.org/), e.g. "10.1105/tpc.114.131607," not "https://doi.org/10.1105/tpc.114.131607"
     pmid:  # Either search for your paper on PubMed, or use the "get_citations.pl" script in a new document to find pmid based on doi (or vice versa!). E.g. "25549672."
   - citation:  # Additional citation of a paper providing more information.
     doi:
@@ -94,13 +93,13 @@ traits:
   - entity_name: starch content
     entity: TO:0000696
 references:
-  - citation: Tang, Su et. al., 2017
+  - citation: Tang, Su et al., 2017
     doi: 10.1093/jxb/erw425
     pmid: 28204559
-  - citation: Su, Han et. al., 2018
+  - citation: Su, Han et al., 2018
     doi: 10.3390/ijms19082395
     pmid: 30110937
-  - citation: Zuo, Ikram et. al., 2022
+  - citation: Zuo, Ikram et al., 2022
     doi: 10.1016/j.csbj.2022.06.014
     pmid: 35782726
 ---
@@ -130,10 +129,10 @@ traits:
   - entity_name: starch content
     entity: TO:0000696
 references:
-  - citation: Tang, Su et. al., 2017
+  - citation: Tang, Su et al., 2017
     doi: 10.1093/jxb/erw425
     pmid: 28204559
-  - citation: Su, Han et. al., 2018
+  - citation: Su, Han et al., 2018
     doi: 10.3390/ijms19082395
     pmid: 30110937
 ---